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Genome-wide analysis of Groucho in Drosophila BG3 cells

ABSTRACT: Genome-wide analysis of Groucho in Drosophila BG3 cells

PROVIDER: PRJEB55476 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10093719_1.fastq.gz	Fastqsanger.gz
	ERR10093719_2.fastq.gz	Fastqsanger.gz
	ERR10093720_1.fastq.gz	Fastqsanger.gz
	ERR10093720_2.fastq.gz	Fastqsanger.gz
	ERR10093721_1.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of Groucho in Drosophila BG3 cells

Project description:We have used ChIP followed by high throughput sequencing to profile the genome-wide recruitment of wildtype Groucho (Gro) at high resolution in BG3 Drosophila cells.

2022-09-15 | E-MTAB-12108 | biostudies-arrayexpress

Genome-wide analysis of Groucho in Drosophila Kc167 and S2R+ cell lines

Project description:In this study we have used ChIP followed by high throughput sequencing to profile the genome-wide recruitment of wildtype and non-oligomerizing Groucho (Gro) at high resolution in single cell types (Kc167 and S2R+) using Drosophila cell culture. Our results reveal that Gro is typically recruited to discrete peaks in active chromatin and that blocking Gro oligomerization does not change the width of the peaks to which it is recruited. We have also investigated acetylated histone H3 and H4 and RNA polymerase II profiles around Gro binding sites, along with gene expression, in wildtype, Gro knockdown, Gro-GFP transfected, and non-oligomerizing Gro-GFP transfected Kc167 cells and found that Gro associates with chromatin containing hypoacetylated histones and frequently overlaps the transcription start sites of expressed genes that exhibit strong RNA polymerase pausing.

2014-09-12 | E-MTAB-2316 | biostudies-arrayexpress

Genome-wide analysis of Groucho in Drosophila Kc167 and S2R+ cell lines

Project description:Genome-wide analysis of Groucho in Drosophila Kc167 and S2R+ cell lines

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Impact of depletion of groucho or notch on transcription in Drosophila intestinal stem cells (ISCs).

Project description:Purpose: To analysis impacts of groucho and notch on transcription in Drosophila ISCs by mRNA-seq. Methods: mRNA-seq of RNA extracted from FACS sorted Drosophila ISCs. Results: Groucho loss in ISCs leads to disruption of lateral inhibition,and knocking down notch in ISCs down-regulates expression of e(spl) factors.

2019-03-15 | GSE112331 | GEO

Drosophila melanogaster

Project description:Genome-wide profiling of H3K56ac in Drosophila melanogaster BG3 cell lines

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Drosophila melanogaster

Project description:Genome-wide profiling of Su(H) in Drosophila melanogaster BG3 cell lines

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Global Stable-isotope Tracing Metabolomics Reveals System-wide Metabolic Alternations in Aging Drosophila

Project description:<p>System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. Using Drosophila as an aging model organism, we probe the in vivo tracing kinetics with quantitative information on labeling patterns, extents and rates on a metabolome-wide scale. We curate a system-wide metabolic network to characterize metabolic homeostasis and disclose a system-wide loss of metabolic coordinations that impacts both intra- and inter-tissue metabolic homeostasis significantly during Drosophila aging. Importantly, we reveal an unappreciated metabolic diversion from glycolysis to serine metabolism and purine metabolism as Drosophila aging. The developed technology facilitates a system-level understanding of metabolic regulation in living organisms.</p>

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Project description:The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target-selection and gene activation in each context. To investigate, we partitioned Drosophila chromatin into different states, based on histone modifications, establishing the preferred chromatin conditions for binding of CSL, the Notch pathway transcription factor. While most histone modifications were unchanged by CSL binding or Notch activation, rapid changes in H3K56 acetylation occurred at Notch regulated-enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation are a conserved indicator of enhancer activation, also occurring at mammalian Notch-regulated Hey1 and at Drosophila ecdysone-regulated genes. This core histone modification may therefore underpin the changes in chromatin accessibility needed to promote transcription following signaling activation. H3K56ac profile of BG3 cells in control condition and EGTA treated condition. In total 4 samples, 2 replicates of H3K56ac ChIP in hbss condition and 2 replicates of H3K56ac ChIP in EGTA treated BG3 cells.

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Project description:The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target-selection and gene activation in each context. To investigate, we partitioned Drosophila chromatin into different states, based on histone modifications, establishing the preferred chromatin conditions for binding of CSL, the Notch pathway transcription factor. While most histone modifications were unchanged by CSL binding or Notch activation, rapid changes in H3K56 acetylation occurred at Notch regulated-enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation are a conserved indicator of enhancer activation, also occurring at mammalian Notch-regulated Hey1 and at Drosophila ecdysone-regulated genes. This core histone modification may therefore underpin the changes in chromatin accessibility needed to promote transcription following signaling activation. Su(H) profile of BG3 cells in control condition and EGTA treated condition. In total 8 samples, 4 replicates of Su(H) ChIP in hbss condition and 4 replicates of Su(H) ChIP in EGTA treated BG3 cells.

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Genome-wide chromatin reconstitution with Drosophila embryo extract and nucleosome positioning by CG7372 and su(Hw)

Project description:We have reconstituted chromatin in vitro on a genome-wide level by incubating total genomic Drosophila melanogaster DNA in D. melanogaster preblastoderm embryo extract. We analyzed chromatin reconstituted with 1) extract from wildtype embryos, 2) extract from embryos lacking the chromatin remodeling enzyme subunit Acf , and 3) extract from Acf-mutant embryos supplemented with recombinant ACF (Acf + Iswi). As a comparison, we also reconstituted chromatin on genomic DNA by salt gradient dialysis. We determined nucleosome positions in reconstituted chromatin by MNase-digestion followed by paired-end sequencing of mononucleosomal fragments. We also determined nucleosome positions in D. melanogaster BG3-c2 cells depleted for the proteins su(Hw) and CG7372 by RNA interference.

2018-08-10 | GSE118335 | GEO

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